This analysis and its results are described in the paper "Citizen-science map of the vaginal microbiome", a preprint of which you can find on Research Square.
This code is provided primarily to demonstrate the full analytical pipeline of our study. It can not be run out of the box, and depends on a complex computational environment.
In order to facilitate running this code, I describe here the outline of what is necessary:
There are two primary environments that may be necessary:
1) An environment with a python installation, together with the python BIU library (https://github.com/thiesgehrmann/BIU/). The BIU library has many optional dependencies, but the following are required for this code to work:
* rpy2
* R
* tidyverse
* MCL
* zdk123/SpiecEasi
* numpy
* pandas
* scipy
* seaborn (and matplotlib)
2) an environment with an R installation, together with the R multidiffabundance package (https://github.com/thiesgehrmann/multidiffabundance)
import rpy2
import sys
sys.path.append('/home/thies/repos/BIU/') # Modify this to where you have downloaded the BIU library
import biu
import numpy as np
import pandas as pd
import matplotlib.pylab as plt
plt.rcParams['svg.fonttype'] = 'none'
import seaborn as sns
import scipy
R = biu.R()